selecting the PIO driver on the other hand makes everything work OK
First step: keep the PIO driver.
We have some mysterious cases in which DMA fails, but it is
hard to track down the problem from remote in computer systems over 15 years old, with a mixture of different hardware pieces.
In one case we found an A3640 Rev3.0 card causing malfunction of DMA...
Did any other Zorro III DMA card work in your setup before?
Do you have the "original" A4000d daughter card at hand?
Michael